[gmx-users] Problems with XTC Files

K.A.Feenstra k.a.feenstra at chem.rug.nl
Thu Dec 6 12:44:31 CET 2001

David van der Spoel wrote:
> Problem maybe that something went wrong in writing, but not enough wrong
> to crash the simulation. Could be e.g. an NFS disk.

We have seen this error occasionally, and indeed it seems to be due to
a missing nfs buffer write to the file, i.e. there is a small section
of the file missing in the middle.

> We have no tools to repair xtc files. The only thing you could do is try
> to write a program that scans the files for a magic number (the start of
> each xtc frame is an integer with value 1995). You'd have to scan the file
> byte by byte, and then you should do an extra check to see whether this
> really is the start. Maybe it can be built into gmxcheck.

After one of the occasions, we wrote such a small tool, unfortunately
it was used once and then got lost. Simply scanning for the magic
nubmer, which is a long int (32 bits), should be as good as fool-proof,
chances of getting this number in the trajectory are extremely low,
especially since it contains many zero's and xtc is compressed so 
shouldn't contain many zero's. 


 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
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